rs1800630

Variant names:

• chr6-31574699-C-A
• rs1800630

Your query was ambiguous. Multiple possible variants found:

• chr6-31574699-C-A
• chr6-31574699-C-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.144 in 151,842 control chromosomes in the GnomAD database, including 1,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective (no stars).

• Frequency: Genomes: 𝑓 0.14 (1698 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: protective no assertion criteria provided B:1
• Conservation: PhyloP100: -2.77

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 6-31574699-C-A is Benign according to our data. Variant chr6-31574699-C-A is described in ClinVar as [protective]. Clinvar id is 12390.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_benign, oryginal submission is: [protective].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21898 AN: 151724 Hom.: 1699 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.144 AC: 21905 AN: 151842 Hom.: 1698 Cov.: 31 AF XY: 0.146 AC XY: 10802 AN XY: 74186

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.163

Alfa AF: 0.153 Hom.: 2867

Bravo AF: 0.141

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Significance: protective

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Alzheimer disease, protection against Benign:1

Aug 01, 2006

OMIM

Significance: protective

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.65
DANN	Benign	0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1800630; hg19: chr6-31542476;